Research in twins defines shared features of the human gut microbial communities: variations linked to obesity

December 03, 2008

Trillions of microbes make their home in the gut, where they help to break down and extract energy and nutrients from the food we eat. Yet, scientists have understood little about how this distinctive mix of microbes varies from one individual to the next.

Now, by cataloging the microbial species in the guts of lean and obese, identical and fraternal female twins and their mothers using a new generation of powerful DNA sequencers, researchers at Washington University School of Medicine in St. Louis have discovered that each individual carries a unique collection of bacteria, although the communities are more similar among family members.

When the scientists looked more deeply at the microbes' DNA, they found a striking similarity: The various collections of bacterial species carried a common set of genes that performed key functions to complement those performed by our human genes. The study is available in the advance online Nature.

"Although there are differences in who's there among our individual gut communities, these different assemblages of microbes carry a common core set of genes that perform key functions. These functions supplement those carried out by our human genes," says senior author Jeffrey I. Gordon, M.D., director of Washington University's Center for Genome Sciences.

Furthermore, when the study's lead author Peter Turnbaugh, a graduate student working in Gordon's lab, sequenced the microbial community DNA, or microbiome, of a subset of obese and lean twin pairs, he found that obese individuals had an increased representation of nearly 300 bacterial genes, many of which are devoted to extracting calories from food and processing nutrients. This new evidence supports Gordon's earlier research in mice that established a link between obesity and the efficiency of energy harvest from the diet by gut bacteria.

To compare gut bacterial communities both within and between families, Gordon and his colleagues obtained stool samples from 31 identical twin pairs, 23 fraternal twin pairs and 46 of their mothers. The twins were in their 20s and 30s and of European or African ancestry. Each twin pair was generally either lean or obese as defined by the Body Mass Index (BMI). All twins were born in Missouri, but they now live throughout the country. They are participants in the Missouri Adolescent Female Twins Study, a long-standing study of Missouri-born twins led by Washington University's Andrew Heath, Ph.D., professor of psychiatry, which is designed to decipher the influence of environment versus genetics on aspects of human health.

In the current study, each individual provided stool samples two months apart, enabling the researchers to track fluctuations in bacterial communities over time. The women had not taken antibiotics, which are known to alter the gut community, for at least six months.

Initially, the researchers sequenced a gene found in all microbes. This gene, 16S rDNA, functions as a barcode of life and can be used to catalog the species present in a microbial community without having to culture the bacteria.

Surprisingly, they did not find a single abundant bacterial species shared in the intestines of the study's 154 participants. While family members were more likely to harbor similar collections of bacterial species, the degree of similarity was the same for identical as for fraternal twin pairs, regardless of whether they lived in the same house or in different regions of the United States, the researchers found.

"This suggests that early environmental exposures play a key role in determining which microbes colonize our intestinal tracts," Gordon says. "It appears that we acquire an enormous number of genes - in the form of our microbial genes - from our early environment." These microbial genes, together with our human genes, form our 'metagenome."

The current research is part of the ongoing human microbiome project, which seeks to not only catalog the microbial species and genes associated with healthy bodies and certain disease states, but to understand how our microbial communities function. Microbial cells are estimated to outnumber human cells by a factor of ten to one. Collectively, the microbes are estimated to carry far more than the 20,000 genes that make up the DNA that we inherit from our parents.

"This study opens many doors to areas that are important to explore," Gordon says. "But before we can confidently associate changes in our indigenous microbial communities with risk for certain diseases, it is very important that we define the normal variations that occur in these communities within and between individuals, and the factors that might drive these variations in our microbial ecology. We are interested in understanding how our modern lifestyles, changing cultural traditions, new technologies, and Western diets are shaping our gut microbiome. We should consider another dimension of human evolution, namely that which is occurring at the level of our microbiomes, as our societies undergo rapid transformation. We think that studying twins living in different parts of the world represents a particularly useful way to move this new area of research forward."

The research was supported by the National Institutes of Health, the National Science Foundation, the W.M. Keck Foundation and the Crohn's and Colitis Foundation of America.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R and Gordon JI. A core gut microbiome in obese and lean twins. Online Nature.

Washington University School of Medicine in St. Louis

---

---

	Teaming with Microbes: The Organic Gardener's Guide to the Soil Food Web, Revised Edition by Jeff Lowenfels (Author), Wayne Lewis (Author) The 2011 Garden Writers of America Gold Award for Best Writing/Book proves soil is anything but an inert substance. Healthy soil is teeming with life -- not just earthworms and insects, but a staggering multitude of bacteria, fungi, and other microorganisms. When we use chemical fertilizers, we injure the microbial life that sustains healthy plants, and thus become increasingly dependent on an arsenal of artificial substances, many of them toxic to humans as well as other forms of life. But there is an alternative to this vicious circle: to garden in a way that strengthens, rather than destroys, the soil food web -- the complex world of soil-dwelling organisms whose interactions create a nurturing environment for plants. By eschewing jargon and overly technical language, the authors make...
	March of the Microbes: Sighting the Unseen by John L. Ingraham (Author), Roberto Kolter (Foreword) Though nothing in the natural world would be quite the same without them, microbes go mostly unnoticed. They are the tiny, mighty force behind the pop in Champagne and the holes in Swiss cheese, the granite walls of Yosemite and the white cliffs of Dover, the workings of snowmaking machines, Botox, and gunpowder; and yet we tend to regard them as peripheral, disease-causing, food-spoiling troublemakers. In this book renowned microbiologist John Ingraham rescues these supremely important and ubiquitous microorganisms from their unwonted obscurity by showing us how we can, in fact, see them—and appreciate their vast and varied role in nature and our lives. Though we might not be able to see microbes firsthand, the consequences of their activities are readily apparent to our unaided...
	Microbe by Moselio Schaechter (Author), John L. Ingraham (Author), Frederick C. Neidhardt (Author) "Microbe", a brand-new, general microbiology textbook intended for upper-division undergraduate and beginning graduate courses, is an exciting introduction to the world of microbes. With a distinct ecological and evolutionary orientation, "Microbe" invites readers to partake of the most current advances in the field. Written by prominent scientists with practical teaching, textbook writing, and research experience, this new textbook will engage students in the learning process with its clear, reader-friendly style and unique perspective of the field. This work: emphasizes the roles of microbes in sustaining all life on Earth; presents paradigm-driven material in a clear, reader-friendly style; deals with the complexities of medical microbiology from the standpoint of both the microbe and...
	Deadly Companions: How Microbes Shaped Our History by Dorothy H. Crawford (Author) Combining tales of devastating epidemics with accessible science and fascinating history, Deadly Companions reveals how closely microbes have evolved with us over the millennia, shaping human civilization through infection, disease, and deadly pandemic. Beginning with a dramatic account of the SARS pandemic at the start of the 21st century, Dorothy Crawford takes us back in time to follow the interlinked history of microbes and humanity, offering an up-to-date look at ancient plagues and epidemics, and identifying key changes in the way humans have lived--such as our move from hunter-gatherer to farmer to city-dweller--which made us ever more vulnerable to microbe attack. Showing that how we live our lives today--with increased crowding and air travel--puts us once again at risk, Crawford...
	The Invisible ABC's: Exploring the World of Microbes by Rodney P. Anderson (Author) This book offers a balanced presentation of the microbial world to children in the early school-age years. Using vivid micrographs that show microorganisms shaped as letters of the alphabet, this book teaches children that microorganisms are fascinating life forms that carry out essential activities in our ecosystems to sustain life on Earth. features over 100 superb illustrations of algae, molds, bacteria, and viruses emphasizes the beneficial roles of microorganisms children encounter in their daily activities, from eating bread and cheese to taking medicines presents scientifically accurate information in an age-appropriate format that is both colorful and captivating communicates the size of microorganisms by relating them to items children are familiar with from everyday experiences.
	The Invisible Kingdom: From the Tips of Our Fingers to the Tops of Our Trash, Inside the Curious World of Microbes by Idan Ben-Barak (Author) With the wit of Bill Bryson and the spirit of Natalie Angier, Idan Ben- Barak takes us on a fantastic voyage into the infinitesimal world of microbiology. In The Invisible Kingdom, he introduces us to the amazing lives and workings of genes, proteins, bacteria, and viruses, and the ways in which they interact to shape life on Earth. Exploring everything from radioactive waste and insect sex-change operations to the inner workings of antibiotics, Ben-Barak reveals how important these tiny critters are to all of us. He brings this largely unseen world to life with refreshing analogies and metaphors: cells “pop like bubbles” and bacteria “dream of rain.” On the journey, we learn about the teamwork required to rot human teeth, the origins of diseases, what really goes on inside cow...
	Microbe Hunters by Paul de Kruif (Author) This science classic by Paul de Kruif chronicles the pioneering bacteriological work of the first scientists to see and learn from the microscopic world.   Paul de Kruif's Microbe Hunters is a timeless dramatization of the scientists, bacteriologists, doctors, and medical technicians who discovered microbes and invented the vaccines to counter them. De Kruif reveals the now seemingly simple but really fundamental discoveries of science—for instance, how a microbe was first viewed in a clear drop of rain water, and when, for the first time ever, Louis Pasteur discovered that a simple vaccine could save a man from the ravages of rabies by attacking the microbes that cause it.
	The Good, the Bad, the Slimy: The Secret Life of Microbes (Prime) by Sara L. Latta (Author), Dennis Kunkel (Photographer)
	Microbe by Bill Clem (Author) In 1947, the U.S. Army left behind a secret when they closed Ft. Miles, Delaware. A threat so deadly, they buried it 1000 feet down in the Atlantic Ocean. Now, sixty years later, an oil rig drilling off the coast of Delaware has hit something. Within hours, crew members are dying from a mysterious illness that kills unmercifully. On the opposite coast, Justin Flannigan, an estranged epidemiologist is visited by the director of the CDC who convinces him to come to Delaware to investigate the bizarre illness. But shortly after he begins his investigation, he gets another visit. This time from an eccentric old man who claims to know the origin of the deadly contagion, and soon, Justin begins to suspect there is more to it than what first appeared. It is evolving swiftly, becoming more...
	Alcamo's Microbes and Society, Third Edition (Jones & Bartlett Learning Topics in Biology Series) by Benjamin S. Weeks (Author) Revised and updated to reflected new information in the field, the Third Edition of Alcamo's Microbes and Society is intended for liberal arts students taking a foundation course in the life sciences. It discusses the role of microbes in our everyday lives, from food production to their roll in biotechnology and the numerous other ways that microbes contribute to our world. It goes on to explore such topics as the function of microbes in ecological systems and environmental systems. Coverage of bioterrorism, antibiotic resistance, and microbial disease offer students a broad and current perspective of the extensive impact of various microbes. Consistent with Edward Alcamo's student-friendly writing style, material is presented in a lively format that will engage students and highlight...